Bakshi Lab @ Presidency, Kolkata

Environmental Microbiome

Our research focuses on uncovering the intricate roles of microbial communities in diverse environmental ecosystems. Using metagenomics and comparative genomics approaches, we study soil, plant rhizospheres, and extreme habitats like hot springs to explore the ecological functions and evolutionary adaptations of microbes. We are particularly interested in understanding how microbial communities contribute to ecosystem resilience, nutrient cycling, and influence human health through their interactions with the environment. Our current research interest focuses on examining the dynamics of the microbial resistome across diverse environmental ecosystems in West Bengal, shaped by varying levels of anthropogenic influence. We aim to understand how antibiotic resistance gene and their associated microbial communities evolve over time in response to environmental factors. Through this study, we seek to enhance our understanding of resistome patterns and gain insights into the factors driving the emergence and persistence of antibiotic resistance in the region.

Relevant Publications:

Mukherji, S., Bakshi, U. & Ghosh, A., 2022. Draft genome sequences of hydrocarbon degrading Haloferax sp. AB510, Haladaptatus sp. AB618 and Haladaptatus sp. AB643 isolated from the estuarine sediments of Sundarban mangrove forests, India. 3 Biotech, 12, 204.
Roy, C., Rameez, M.J., Haldar, P.K., Peketi, A., Mondal, N., Bakshi, U., Mapder, T., Pyne, P., Fernandes, S., Bhattacharya, S. and Roy, R., 2020. Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau. Scientific reports, 10(1), pp.1-22.
Roy, C., Bakshi, U., Rameez, M.J., Mandal, S., Haldar, P.K., Pyne, P. and Ghosh, W., 2019. Phylogenomics of an uncultivated, aerobic and thermophilic, photoheterotrophic member of Chlorobia sheds light into the evolution of the phylum Chlorobi. Computational biology and chemistry, 80, pp.206-216.
Bhattacharyya, C., Bakshi, U., Mallick, I., Mukherji, S., Bera, B. and Ghosh, A., 2017. Genome-guided insights into the plant growth promotion capabilities of the physiologically versatile Bacillus aryabhattai strain AB211. Frontiers in microbiology, 8, p.411.

Human Microbiome

The human microbiome is central to our research focus on understanding its role in health and disease. Our objective is to elucidate how microbial communities across various body niches influence critical metabolic pathways and interact with host systems. Our work combines high-throughput omics data with computational biology to identify microbial biomarkers, track microbiome perturbations, and predict clinical outcomes. Currently, we are investigating microbiome alterations in an Eastern Indian cohort of oral squamous cell carcinoma patients, comparing their microbial profiles to those of healthy individuals to identify disease-associated microbial signatures. In parallel, as part of a translational research initiative, we are collaborating on a project to evaluate the effects of a novel nanofiber-reinforced composite on salivary microbiome dynamics. This study focuses on characterizing changes in the microbial community structure and function following exposure to the composite material, with the broader goal of understanding its potential impact on oral health.

Relevant Publications:

Gupta, V. K., Bakshi, U., Chang, D., Lee, A. R., Davis III, J. M., Chandrasekaran, S., & Sung, J. 2022. TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes. Msystems, 7(6), e00925-22.
Gupta, V. K., Cunningham, K. Y., Hur, B., Bakshi, U., Huang, H., Warrington, K. J., Taneja, V., Myasoedova, E., Davis, J. M., and Sung, J., 2021. Gut microbial determinants of clinically important improvement in patients with rheumatoid arthritis. Genome medicine, 13(1), 149.
Gupta, V.K., Kim, M., Bakshi, U., Cunningham, K.Y., Davis, J.M., Lazaridis, K.N., Nelson, H., Chia, N. and Sung, J., 2020. A predictive index for health status using species-level gut microbiome profiling. Nature Communications, 11(1):4635.
Bakshi, U., Sarkar, M., Paul, S. and Dutta, C., 2016. Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach–Identification of pathogen–specific and habitat-specific genes. Scientific reports, 6, p.38648.

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